Both players have been ruled out of the North London derby through injury, which takes place at White Hart Lane on Saturday lunchtime, but Thompson has insisted that if manager Arsene Wenger had the option to play just one of the duo, he would choose Cech.
Thompson feels that the former Chelsea stopper's experience and communication skills have played a significant part in Arsenal remaining in the Premier League title race throughout the season.
The former Liverpool boss also insists that the Gunners cannot afford to let slip an opportunity to win the championship for the first time since 2004.
Thompson said: "The biggest miss is going to be Petr Cech. He has proved the missing link to this Arsenal side and everyone is saying that this is Arsenal's best year.
"They are the best-equipped side and if they don't win the league, it will be a massive failure on behalf of the manager and the players not taking advantage of it.
"Cech has put them in that position and the other players are not responding. He is a great organiser, he talks to everyone at the back. They could be vulnerable at the weekend."
Since his transfer from Stamford Bridge in the summer, Cech has been an ever-present in top-flight fixtures, keeping 12 clean sheets.
His hamstring problem gives an opportunity to David Ospina, who has played five times in all competitions since being demoted to the bench upon Cech's arrival.
Arsenal can move level on points with Spurs in second position if they can get the better of their arch rivals.